ArticleProtein science : a publication of the Protein Society2012
Modeling large regions in proteins: applications to loops, termini, and folding.
Article in Protein science : a publication of the Protein Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 23 citations in OpenAlex.
- Computational design of structured loops for new protein functions.Biological chemistry · 2019Review
- Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Indel reliability in indel-based phylogenetic inference.Genome biology and evolution · 2014Article
- Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction.Proteins · 2014Article
- Article
- Simplified protein models: predicting folding pathways and structure using amino acid sequences.Physical review letters · 2013Article
- Detecting protein candidate fragments using a structural alphabet profile comparison approach.PloS one · 2013Article
- De novo prediction of protein folding pathways and structure using the principle of sequential stabilization.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized).Journal of molecular biology · 2012Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Template-based methods for predicting protein structure provide models for a significant portion of the protein but often contain insertions or chain ends (InsEnds) of indeterminate conformation. The local structure prediction "problem" entails modeling the InsEnds onto the rest of the protein. A well-known limit involves predicting loops of ≤12 residues in crystal structures. However, InsEnds may contain as many as ~50 amino acids, and the template-based model of the protein itself may be imperfect. To address these challenges, we present a free modeling method for predicting the local structure of loops and large InsEnds in both crystal structures and template-based models. The approach uses single amino acid torsional angle "pivot" moves of the protein backbone with a C(β) level representation. Nevertheless, our accuracy for loops is comparable to existing methods. We also apply a more stringent test, the blind structure prediction and refinement categories of the CASP9 tournament, where we improve the quality of several homology based models by modeling InsEnds as long as 45 amino acids, sizes generally inaccessible to existing loop prediction methods. Our approach ranks as one of the best in the CASP9 refinement category that involves improving template-based models so that they can function as molecular replacement models to solve the phase problem for crystallographic structure determination.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.